Open thesamuanels opened 6 months ago
What was your command and input? I found that many errors can be fixed by playing around with the python version.
Frank
On Mon, Jan 29, 2024, 8:22 PM DGian @.***> wrote:
Hello, I've been trying to run ViralRecall, both using the test provided and with my own data, but it always gives me the following error:
Traceback (most recent call last): File "/opt/viralrecall/viralrecall.py", line 733, in
status = main() File "/opt/viralrecall/viralrecall.py", line 725, in main run_program(newinput, newproject, database, window, phagesize, minscore, minhit, evalue, cpus, plotflag, redo, flanking, batch, summary_file, contiglevel) File "/opt/viralrecall/viralrecall.py", line 475, in run_program summary = summary.append(data) File "/opt/Anaconda3/envs/viralrecall/lib/python3.10/site-packages/pandas/core/generic.py", line 5989, in getattr return object.getattribute(self, name) AttributeError: 'DataFrame' object has no attribute 'append'. Did you mean: '_append'? Any idea what the issue might be?
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The input for that specific output was:
python /opt/viralrecall/viralrecall.py -i test -c -p viralrecall.out -b -e 1e-5
However, I got the same error when running:
python viralrecall.py -i examples/arm29B.fna -p test_outdir -t 2 -f
I have downgraded to python 3.5.6, now when running
python /opt/viralrecall/viralrecall.py -i test -c -p viralrecall.out -b -e 1e-5
I've obtained:
Running viralrecall on ALA.Apr2023.130_S8_metabat2.7.fa and output will be deposited in viralrecall.out/ALA.Apr2023.130_S8_metabat2.7.fa
Traceback (most recent call last):
File "/opt/viralrecall/viralrecall.py", line 733, in <module>
status = main()
File "/opt/viralrecall/viralrecall.py", line 725, in main
run_program(newinput, newproject, database, window, phagesize, minscore, minhit, evalue, cpus, plotflag, redo, flanking, batch, summary_file, contiglevel)
File "/opt/viralrecall/viralrecall.py", line 401, in run_program
df = pandas.concat([df, s1], axis=1, sort=True)
TypeError: concat() got an unexpected keyword argument 'sort'
Yeah I think this is an issue with the Pandas version then. They changed the way that data frames can be sorted. So maybe downgrade the pandas version? Sorry I can't be more specific. Frank
On Tue, Jan 30, 2024, 5:02 PM DGian @.***> wrote:
The input for that specific output was: python /opt/viralrecall/viralrecall.py -i test -c -p viralrecall.out -b -e 1e-5 However, I got the same error when running: python viralrecall.py -i examples/arm29B.fna -p test_outdir -t 2 -f
I have downgraded to python 3.5.6, now when running python /opt/viralrecall/viralrecall.py -i test -c -p viralrecall.out -b -e 1e-5 I've obtained:
Running viralrecall on ALA.Apr2023.130_S8_metabat2.7.fa and output will be deposited in viralrecall.out/ALA.Apr2023.130_S8_metabat2.7.fa Traceback (most recent call last): File "/opt/viralrecall/viralrecall.py", line 733, in status = main() File "/opt/viralrecall/viralrecall.py", line 725, in main run_program(newinput, newproject, database, window, phagesize, minscore, minhit, evalue, cpus, plotflag, redo, flanking, batch, summary_file, contiglevel) File "/opt/viralrecall/viralrecall.py", line 401, in run_program df = pandas.concat([df, s1], axis=1, sort=True) TypeError: concat() got an unexpected keyword argument 'sort'` And when running
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Solved! Thanks. We actually had an older version of pandas in our conda environment. It works now with pandas 0.23.0
Great! Glad it worked out.
Frank
On Tue, Jan 30, 2024, 7:20 PM DGian @.***> wrote:
Solved! Thanks. We actually had an older version of pandas in our conda environment. It works now with pandas 0.23.0
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Hello, I've been trying to run ViralRecall, both using the test provided and with my own data, but it always gives me the following error:
Traceback (most recent call last):
File "/opt/viralrecall/viralrecall.py", line 733, in <module>
status = main()
File "/opt/viralrecall/viralrecall.py", line 725, in main
run_program(newinput, newproject, database, window, phagesize, minscore, minhit, evalue, cpus, plotflag, redo, flanking, batch, summary_file, contiglevel)
File "/opt/viralrecall/viralrecall.py", line 475, in run_program
summary = summary.append(data)
File "/opt/Anaconda3/envs/viralrecall/lib/python3.10/site-packages/pandas/core/generic.py", line 5989, in __getattr__
return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'append'. Did you mean: '_append'?
Any idea what the issue might be?